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The basic thing I don't understand is why anyone would ever want to set the contour level of a Fo-type map (ie one which tries to estimate the "best" electron density representing the structure, eg 2mFo-DFc) in terms of its RMSD. It makes no sense and never has. There is no legitimate expectation of what the RMSD should be.
For a _difference_ map, where the expectation in the case of perfection is that the map should be flat and indeed zero, the RMSD can be used sensibly to look for features which deviate "significantly" from zero. But then so can e/A^3.
In practice, in the end it isn't really important, as when you are looking at maps on the screen you set the contour level to whatever shows the features that you are interested in. Then it doesn't matter whether the units of the map are in e/A^3, RMSD or elephants.
... but this thread does allow me to let off some steam. Phil
